A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins
Figure 1
Examples of pocket alignments according to APoc.
(A–F) Six ADP-binding pockets taken from six different protein structures (green) are aligned to a common ADP-binding pocket from the checkpoint protein kinase Chk2 (purple). In each snapshot, the two protein structures are shown in cartoon representations, and the corresponding bound-ligands are shown in cyan and red licorice representations, respectively. For clarity, non-pocket regions are shown in transparent purple in Chk2, and in transparent grey in the other proteins, whereas pocket regions are shown in solid purple in Chk2 and solid green in the other cases. Aligned pocket Cα atoms are shown as spheres. An enlarged view of the pocket alignment is displayed on the right. The top label denotes the name of the protein and its PDB accession code in parentheses; and the bottom label denotes the corresponding PS-score, P-value, RMSD of aligned atoms, and the TM-score. Molecular images were created with VMD [56]. They were taken in the same view at Chk2.